Univ.-Prof. Dr. David Berry

The intestinal microbiota lives in an intimate symbiosis with its animal or human host and provides services such as vitamin production, breakdown of refractory dietary compounds, immune training, and protection against pathogens. Shifts in the intestinal microbiota have been associated with many diseases, but in most cases detailed understanding of the causes and consequences of these changes is still lacking. My group is interested in the function of the gut microbiota in health and disease and employs an ecological and evolutionary perspective as well as an organismal view by studying the physiology of key gut microbiota members.

Intestinal tissue is protected from direct exposure to a vast number of microbes by a thin layer of secreted mucus. This mucus serves not only as a barrier for the host, but also a nutrient source and habitat for a distinct group of microbes. The mucus-associated microbiota is a key group as it can modify the penetrability of the mucus layer, which has implications for pathogen entry. Due to its proximity to the tissue, it may also play a key role in chemical signaling and interactions with the host.

Intestinal microbiology is currently being driven to a large extent by sequencing based methods such as metagenomics and metatranscriptomics. Complementary tools are now needed to deeper probe microbial activity and interactions. We are developing novel single cell isotope labeling tools that allow detailed insights into substrate partitioning and niche competition among individual intestinal microbiota members, including incoming pathogens (Stecher, Berry, and Loy, 2013).

RESEARCH TOPICS

Function of the intestinal microbiota in health and disease

Novel modeling approaches to study microbial communities

Development of molecular and isotope-labeling methods for studying uncultivated microorganisms in their natural environment

RECENT PROJECTS

Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members, though many questions remain about their validity and performance. Using a simulation-based approach, we evaluated how well networks reveal underlying interactions. We found that co-occurrence networks can recapitulate interaction networks under certain conditions, and also identified topological features associated with keystone species in co-occurrence networks. This work provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets (Berry and Widder, 2014).

Single cell stable isotope probing of the gut microbiota. Microbes live almost exclusively in complex communities, and it remains a major challenge to identify the activity of microbial cells under natural conditions. We have developed tools based on single cell stable isotope probing to address this. Using fluorescence in situ hybridization combined with high-resolution secondary ion mass spectrometry (NanoSIMS) we were able to identify microbial cells that had degraded secreted mucosal proteins (Berry et al., 2013). Recently, we were able to use heavy water as a universal activity marker combined with Raman microspectroscopy to profile the in situ activity of two mucus-degrading species, Akkermansia muciniphila and Bacteroides acidifaciens, to a range of amended nutrients (Berry et al., 2015).

Microbiota and intestinal inflammation. Human inflammatory bowel diseases are thought to be affected by the gut microbiota and are characterized by an altered gut microbiota composition (Berry and Reinisch, 2013). We have been investigating this relationship using mouse colitis models (Berry et al., 2012; Schwab et al., 2014) as well as by evaluating the potential of fecal microbiota transplantation for the treatment of ulcerative colitis in humans (Angelberger et al., 2013).

JOINING THE TEAM

Information on open research positions can be found here. If you are interested in joining our team with your own fellowship, please check out our PhD & postdoc program and get in touch with David for details.